Use of the cards gives a rough "eyeball" evaluation of student learning throughout a lecture. Using the cards, for me at least, also provides a gauge of attendance as well and also if it waxes or wanes during the class period.
For many years I have resisted using clickers, mainly because at our university there is no standard universal clicker. I wanted to keep student costs as low as possible but also desired the type of live feedback during a lecture that clicker questions can provide. In both my general chem. (200-300 students) and upper division courses (50-75 students), I now pass out 4 or 5 colored notecards on the first day of class and make sure everyone has one of each color. I then do clicker style questions and color code the different answer choices in powerpoint and ask them to hold up their choice after 15-60 seconds depending on the question. This has worked well to provide me instant feedback on difficult topics and doesn't end up singling out any particular student, which most students detest in larger lecture courses.
Students are able to provide feedback to the instructor on questions quickly and "anonymously" and allow one to adjust the direction of a lecture on the fly.
I typically use between 4-6 clicker questions during a 50 minute lecture. I'm sure someone could use more/less based on an individual's needs. I think the key is to use clicker style questions from the beginning of the class on a daily basis to remind students to bring the note cards in a book/binder/bag. This is really the only problem I have encountered- students often forget their cards. It is probably a wash though, as I'm sure students can also forget clickers.